R Notebook

Medicago GWAS Pipeline

Given a set of trait files (cleaned and normlised), perform a standard GWAS + population structure analysis. This pipeline is maintained at https://github.com/nickb-/GWASPipeline. For more detailed explanations please see the Sandpit directory of the repository.

Trait Preparation

We assume that the trait files are saved in a folder named “Traits”. This pipeline will ONLY work with a single trait file. If you have multiple traits, you should create a combined file, with one column for each trait. See Sandpit/GWAS_Trait_Wrangling.html for a worked example.

Analyses will be performed in PLINK thus, we assume that there is a trait (phenotype) file that conforms to plink’s specifications. Specifically: {FID, IID, trait_one, trait_two...}. Each column should be TAB or SPACE separated. For more info: https://www.cog-genomics.org/plink2/input#pheno. An example trait file is shown below:

FID	IID	StantonFloweringDate	FTa1	FTa2	FIRSTFLWR	VRN_FT1
0	HM001	-6.29	0.013	-9.000	-9	-9.000
0	HM002	-3.29	0.000	-9.000	103	-1.338
0	HM003	2.08	0.000	-5.829	-9	-0.660
0	HM004	1.58	0.032	-9.000	-9	-9.000
0	HM005	2.28	0.010	-9.000	-9	-2.323
0	HM006	2.33	0.009	-9.000	-9	-4.448

Genotypes

We assume that the Genotypes are either VCF or BCF files, saved in a folder named “Genotypes”. Genotypes may be split into separate files per chromosome, or one large file.

The default QC parameters are as follows:

• reject SNPs with call frequency < 90%
  
• reject SNPS with minor allele frequency (MAF) < 0.03

These parameters can be changed in the Setup section below. This pipeline will handle the rest for you.

GWAS

This pipeline will:

• plot the trait data (saved in Results/Visualisations)
  
• determine the population structure
  
• perform a standard GWAS adjusted for population structure, using plink
  
• results of the association tests, Q-Q plots and manhattan plots will be saved in the Results directory.

PLINK Setup

You will need PLINK to run this pipeline. To get PLINK up and running perform the following:

1. Download the appropriate version of plink from here: https://www.cog-genomics.org/plink2
   
2. Unpack the zipped plink folder somewhere convenient
   
3. Make sure you set the plink_directory paramter in the Setup section below

Running the pipeline

Review the Setup section below:

1. Change the working directory as appropriate (to the directory where you have the PLINK, Genotypes and Traits folders)
   
2. Review the Genotype QC parameters, and change as appropriate (defaults are usually sufficient)
   
3. Run each cell as required
   
4. Have fun :)

---

Setup

Set the home_ and plink_ variables below. Review the parameters list, changing where appropriate. Then run this cell.

# set the home & plink directory (please no spaces or funny characters)
home_ <- "/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline"
plink_ <- "/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/PLINK/plink"
# Genotype QC settings
parameters <- list(
    call_rate = 0.10,                       # rejects SNPs with more than this number of missing calls
    maf = 0.02,                             # rejects SNPs with a MAF < this threshold
    pop_struct_dimensions = 10,             # the number of principal components for population structure
    file_format = "bcf"
)

Housekeeping

There is no need to change anything in this cell. Run the following cell, it will install required pacakges, test for plink and setup the working directory.

# install & load packages
options(repos = "http://cran.uk.r-project.org")
if (!require(data.table)) {    
    install.packages("data.table")
}

Loading required package: data.table
data.table 1.9.6  For help type ?data.table or https://github.com/Rdatatable/data.table/wiki
The fastest way to learn (by data.table authors): https://www.datacamp.com/courses/data-analysis-the-data-table-way

if (!require(gridExtra)) {
    install.packages("gridExtra")
}

Loading required package: gridExtra

if (!require(ggplot2)) {
    install.packages("ggplot2")
}

Loading required package: ggplot2

if (!require(qqman)) {
    install.packages("qqman")
}

Loading required package: qqman

For example usage please run: vignette('qqman')

Citation appreciated but not required:
Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165 (2014).

library(ggplot2)
library(data.table)
library(gridExtra)
library(qqman)
# setup the working directory
setwd(home_)

The working directory was changed to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the the working directory for notebook chunks.

if (!dir.exists("./Results")) {
    dir.create(file.path(home_, "Results"))
}
if (!dir.exists("./Results/Visualisations")) {
    dir.create(file.path(home_, "Results/Visualisations"))
}
if (!dir.exists("./ScratchSpace")) {
    dir.create(file.path(home_, "ScratchSpace"))
}
# test plink installation
if (!capture.output({ cat(system(sprintf("%s --version", plink_))) }) == 0) {
    
    cat(sprintf("
        --------------------------------------------------------------------------------
                                      !!!! WARNING !!!! 
        
        PLINK not found. Please review the plink_ directory in the Setup section.
        --------------------------------------------------------------------------------
    ", plink_))
    
}

PLINK v1.90b3.31 64-bit (3 Feb 2016)

# extract trait files and genotype files  
trait_files <- list.files("./Traits")
genotype_files <- list.files("./Genotypes")
if (any(c(length(trait_files) < 1, length(genotype_files) < 1))) {
    
    cat(sprintf("
        --------------------------------------------------------------------------------
                                      !!!! WARNING !!!! 
        
        Something has gone wrong with the trait and/or the genotype files. Please review.
        There are %s trait files and %s genotype files. 
        --------------------------------------------------------------------------------
    ", length(trait_files), length(genotype_files)))
    
} else {
    "Ready to proceed..."
}

[1] "Ready to proceed..."

Trait Visualisation

Optional. If you would like to visualise your traits, run the cell below. It will create boxplots of each trait and save these in the Results directory. We recommend running this step as a sanity check and for future reference.

for (file_ in trait_files) {
    
    file_out <- strsplit(file_, "\\.")[[1]][1]
    
    tmp <- fread(sprintf("%s/Traits/%s", home_, file_, na.strings = '-9'))
    tmp <- melt(tmp, id.vars = c("FID", "IID"))
    
    
    g <- ggplot(tmp, aes(x = 1, y = value)) +
             geom_boxplot() +
             facet_wrap(~variable, scales = "free_y") +
             theme_minimal()
    ggsave(file = sprintf("%s/Results/Visualisations/%s.png", home_, file_out), g)
   
}

GWAS Pipeline

The following cell will run the GWAS. There is no need to change anything in this cell. The GWAS pipeline will operate on each chromosome separately and perform the following:

- genotype QC: filter on call rate and MAF  
- estimate population structure (this is to be reviewed in the future)   
- perform association study  

All intermediate results will be saved in the Pipeline/ScratchSpace directory. This directory will get large (possibly ~ 10 - 20 GB).

setwd(sprintf("%s/ScratchSpace", home_))

The working directory was changed to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the the working directory for notebook chunks.

start_time <- Sys.time()
get_columns <- function (x, dir_ = sprintf("%s/Traits", home_)) {
    tmp <- fread(sprintf("%s/%s", dir_, x))
    return (colnames(tmp)[-c(1, 2)])
}
all_traits <- get_columns(trait_files)
pheno_file <- sprintf("%s/Traits/%s", home_, trait_files)
# perform GWAS
for (geno_ in genotype_files) {
        
        chromosome <- strsplit(geno_, "\\.")[[1]][1]
        assoc_results <- sprintf("%s/ScratchSpace/%s", home_, chromosome)
        
        # QC steps
        cat(sprintf("
            Performing QC steps on genotype file: %s
        ", geno_))
        
        geno_file <- sprintf("%s/Genotypes/%s", home_, geno_)
        cmd <- sprintf("
        %s --%s %s \\
              --const-fid \\
              --allow-extra-chr \\
              --keep %s \\
              --geno %s \\
              --maf %s \\
              --make-bed \\
              --out qc_genotypes
        ", plink_, parameters$file_format, geno_file, pheno_file, parameters$call_rate, parameters$maf
        )
        
        write(cmd, file = "plink.cmd")
        system("bash plink.cmd")
        
        # population structure
        cat("Estimating population structure...")
        cmd <- sprintf("%s --bfile %s --pca %s --out population_structure", plink_, "qc_genotypes", parameters$pop_struct_dimensions)
        system(cmd)
    
        # Association test
        cat("Performing association test...")
        cmd <- sprintf("
        %s --bfile %s \\
                    --linear \\
                    --adjust \\
                    --pheno %s \\
                    --all-pheno \\
                    --covar %s \\
                    --allow-no-sex \\
                    --out %s
        ", plink_, "qc_genotypes", pheno_file, "population_structure.eigenvec", assoc_results)
        system(cmd)
        
}

            Performing QC steps on genotype file: chr1-filtered-set-2014Apr15.bcf
        PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to qc_genotypes.log.
Options in effect:
  --allow-extra-chr
  --bcf /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Genotypes/chr1-filtered-set-2014Apr15.bcf
  --const-fid
  --geno 0.1
  --keep /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined
  --maf 0.02
  --make-bed
  --out qc_genotypes

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--bcf: qc_genotypes-temporary.bed + qc_genotypes-temporary.bim +
qc_genotypes-temporary.fam written.
4978489 variants loaded from .bim file.
262 people (0 males, 0 females, 262 ambiguous) loaded from .fam.
Ambiguous sex IDs written to qc_genotypes.nosex .
--keep: 225 people remaining.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate in remaining samples is 0.780208.
3285907 variants removed due to missing genotype data (--geno).
1372755 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
319827 variants and 225 people pass filters and QC.
Note: No phenotypes present.
--make-bed to qc_genotypes.bed + qc_genotypes.bim + qc_genotypes.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
Estimating population structure...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to population_structure.log.
Options in effect:
  --bfile qc_genotypes
  --out population_structure
  --pca 10

15488 MB RAM detected; reserving 7744 MB for main workspace.
319827 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to population_structure.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939744.
319827 variants and 225 people pass filters and QC.
Note: No phenotypes present.

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Relationship matrix calculation complete.
[extracting eigenvalues and eigenvectors]
--pca: Results saved to population_structure.eigenval and
population_structure.eigenvec .
Performing association test...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.log.
Options in effect:
  --adjust
  --all-pheno
  --allow-no-sex
  --bfile qc_genotypes
  --covar population_structure.eigenvec
  --linear
  --out /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15
  --pheno /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined

15488 MB RAM detected; reserving 7744 MB for main workspace.
319827 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.nosex
.
225 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked.
--covar: 10 covariates loaded.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939744.
319827 variants and 225 people pass filters and QC.
Phenotype data is quantitative.
225 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.GH2_FlDate.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.24415.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (319827 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.GH2_FlDate.assoc.linear.adjusted
.
56 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.nodestofloweringV.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.02575.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (301489 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.nodestofloweringV.assoc.linear.adjusted
.
86 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.NV_FTa1.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.03815.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (312574 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.NV_FTa1.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.FTa1_Expn.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.05668.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (313707 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.FTa1_Expn.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.05581.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (313707 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear.adjusted
.
74 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.03908.
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/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear.adjusted
.
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Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.12727.
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/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear.adjusted
.
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Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.SOC1c.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.0586.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (317242 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.SOC1c.assoc.linear.adjusted
.
48 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.SOC1c_V.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (297184 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr1-filtered-set-2014Apr15.SOC1c_V.assoc.linear.adjusted
.

            Performing QC steps on genotype file: chr2-filtered-set-2014Apr15.bcf
        PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to qc_genotypes.log.
Options in effect:
  --allow-extra-chr
  --bcf /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Genotypes/chr2-filtered-set-2014Apr15.bcf
  --const-fid
  --geno 0.1
  --keep /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined
  --maf 0.02
  --make-bed
  --out qc_genotypes

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--bcf: qc_genotypes-temporary.bed + qc_genotypes-temporary.bim +
qc_genotypes-temporary.fam written.
4331584 variants loaded from .bim file.
262 people (0 males, 0 females, 262 ambiguous) loaded from .fam.
Ambiguous sex IDs written to qc_genotypes.nosex .
--keep: 225 people remaining.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate in remaining samples is 0.76894.
2937753 variants removed due to missing genotype data (--geno).
1109997 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
283834 variants and 225 people pass filters and QC.
Note: No phenotypes present.
--make-bed to qc_genotypes.bed + qc_genotypes.bim + qc_genotypes.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
Estimating population structure...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to population_structure.log.
Options in effect:
  --bfile qc_genotypes
  --out population_structure
  --pca 10

15488 MB RAM detected; reserving 7744 MB for main workspace.
283834 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to population_structure.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939427.
283834 variants and 225 people pass filters and QC.
Note: No phenotypes present.

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Relationship matrix calculation complete.
[extracting eigenvalues and eigenvectors]
--pca: Results saved to population_structure.eigenval and
population_structure.eigenvec .
Performing association test...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.log.
Options in effect:
  --adjust
  --all-pheno
  --allow-no-sex
  --bfile qc_genotypes
  --covar population_structure.eigenvec
  --linear
  --out /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15
  --pheno /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined

15488 MB RAM detected; reserving 7744 MB for main workspace.
283834 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.nosex
.
225 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked.
--covar: 10 covariates loaded.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939427.
283834 variants and 225 people pass filters and QC.
Phenotype data is quantitative.
225 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.GH2_FlDate.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.22582.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (283834 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.GH2_FlDate.assoc.linear.adjusted
.
56 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.nodestofloweringV.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.0582.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (268660 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.nodestofloweringV.assoc.linear.adjusted
.
86 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.NV_FTa1.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (277334 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.NV_FTa1.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.FTa1_Expn.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.01006.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (278695 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.FTa1_Expn.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.01181.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (278695 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear.adjusted
.
74 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.11086.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (276502 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.07016.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (278695 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear.adjusted
.
120 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.SOC1c.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (281752 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.SOC1c.assoc.linear.adjusted
.
48 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.SOC1c_V.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.02371.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (265938 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr2-filtered-set-2014Apr15.SOC1c_V.assoc.linear.adjusted
.

            Performing QC steps on genotype file: chr3-filtered-set-2014Apr15.bcf
        PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to qc_genotypes.log.
Options in effect:
  --allow-extra-chr
  --bcf /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Genotypes/chr3-filtered-set-2014Apr15.bcf
  --const-fid
  --geno 0.1
  --keep /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined
  --maf 0.02
  --make-bed
  --out qc_genotypes

15488 MB RAM detected; reserving 7744 MB for main workspace.

--bcf: 1k variants complete.
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--bcf: qc_genotypes-temporary.bed + qc_genotypes-temporary.bim +
qc_genotypes-temporary.fam written.
5424868 variants loaded from .bim file.
262 people (0 males, 0 females, 262 ambiguous) loaded from .fam.
Ambiguous sex IDs written to qc_genotypes.nosex .
--keep: 225 people remaining.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate in remaining samples is 0.75449.
3774267 variants removed due to missing genotype data (--geno).
1301349 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
349252 variants and 225 people pass filters and QC.
Note: No phenotypes present.
--make-bed to qc_genotypes.bed + qc_genotypes.bim + qc_genotypes.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
Estimating population structure...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to population_structure.log.
Options in effect:
  --bfile qc_genotypes
  --out population_structure
  --pca 10

15488 MB RAM detected; reserving 7744 MB for main workspace.
349252 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to population_structure.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.938834.
349252 variants and 225 people pass filters and QC.
Note: No phenotypes present.

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Relationship matrix calculation complete.
[extracting eigenvalues and eigenvectors]
--pca: Results saved to population_structure.eigenval and
population_structure.eigenvec .
Performing association test...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.log.
Options in effect:
  --adjust
  --all-pheno
  --allow-no-sex
  --bfile qc_genotypes
  --covar population_structure.eigenvec
  --linear
  --out /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15
  --pheno /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined

15488 MB RAM detected; reserving 7744 MB for main workspace.
349252 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.nosex
.
225 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked.
--covar: 10 covariates loaded.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.938834.
349252 variants and 225 people pass filters and QC.
Phenotype data is quantitative.
225 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.GH2_FlDate.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.29574.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (349252 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.GH2_FlDate.assoc.linear.adjusted
.
56 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.nodestofloweringV.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.14875.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (329837 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.nodestofloweringV.assoc.linear.adjusted
.
86 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.NV_FTa1.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.02837.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (342003 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.NV_FTa1.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.FTa1_Expn.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.20949.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (342739 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.FTa1_Expn.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.20404.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (342739 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear.adjusted
.
74 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.03318.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (339881 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.0849.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (342739 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear.adjusted
.
120 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.SOC1c.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.14003.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (346804 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.SOC1c.assoc.linear.adjusted
.
48 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.SOC1c_V.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (325786 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr3-filtered-set-2014Apr15.SOC1c_V.assoc.linear.adjusted
.

            Performing QC steps on genotype file: chr4-filtered-set-2014Apr15.bcf
        PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to qc_genotypes.log.
Options in effect:
  --allow-extra-chr
  --bcf /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Genotypes/chr4-filtered-set-2014Apr15.bcf
  --const-fid
  --geno 0.1
  --keep /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined
  --maf 0.02
  --make-bed
  --out qc_genotypes

15488 MB RAM detected; reserving 7744 MB for main workspace.

--bcf: 1k variants complete.
--bcf: 2k variants complete.
--bcf: 3k variants complete.
--bcf: 4k variants complete.
--bcf: 5k variants complete.
--bcf: 6k variants complete.
--bcf: 7k variants complete.
--bcf: 8k variants complete.
--bcf: 9k variants complete.
--bcf: 10k variants complete.
--bcf: 11k variants complete.
--bcf: 12k variants complete.
--bcf: 13k variants complete.
--bcf: 14k variants complete.
--bcf: 15k variants complete.
--bcf: 16k variants complete.
--bcf: 17k variants complete.
--bcf: 18k variants complete.
--bcf: 19k variants complete.
--bcf: 20k variants complete.
--bcf: 21k variants complete.
--bcf: 22k variants complete.
--bcf: 23k variants complete.
--bcf: 24k variants complete.
--bcf: 25k variants complete.
--bcf: 26k variants complete.
--bcf: 27k variants complete.
--bcf: 28k variants complete.
--bcf: 29k variants complete.
--bcf: 30k variants complete.
--bcf: 31k variants complete.
--bcf: 32k variants complete.
--bcf: 33k variants complete.
--bcf: 34k variants complete.
--bcf: 35k variants complete.
--bcf: 36k variants complete.
--bcf: 37k variants complete.
--bcf: 38k variants complete.
--bcf: 39k variants complete.
--bcf: 40k variants complete.
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--bcf: qc_genotypes-temporary.bed + qc_genotypes-temporary.bim +
qc_genotypes-temporary.fam written.
5414544 variants loaded from .bim file.
262 people (0 males, 0 females, 262 ambiguous) loaded from .fam.
Ambiguous sex IDs written to qc_genotypes.nosex .
--keep: 225 people remaining.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate in remaining samples is 0.775827.
3609774 variants removed due to missing genotype data (--geno).
1450645 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
354125 variants and 225 people pass filters and QC.
Note: No phenotypes present.
--make-bed to qc_genotypes.bed + qc_genotypes.bim + qc_genotypes.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
Estimating population structure...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to population_structure.log.
Options in effect:
  --bfile qc_genotypes
  --out population_structure
  --pca 10

15488 MB RAM detected; reserving 7744 MB for main workspace.
354125 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to population_structure.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939242.
354125 variants and 225 people pass filters and QC.
Note: No phenotypes present.

60 markers complete.
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Relationship matrix calculation complete.
[extracting eigenvalues and eigenvectors]
--pca: Results saved to population_structure.eigenval and
population_structure.eigenvec .
Performing association test...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.log.
Options in effect:
  --adjust
  --all-pheno
  --allow-no-sex
  --bfile qc_genotypes
  --covar population_structure.eigenvec
  --linear
  --out /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15
  --pheno /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined

15488 MB RAM detected; reserving 7744 MB for main workspace.
354125 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.nosex
.
225 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked.
--covar: 10 covariates loaded.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939242.
354125 variants and 225 people pass filters and QC.
Phenotype data is quantitative.
225 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.GH2_FlDate.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.22362.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (354125 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.GH2_FlDate.assoc.linear.adjusted
.
56 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.nodestofloweringV.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (336090 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.nodestofloweringV.assoc.linear.adjusted
.
86 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.NV_FTa1.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (346385 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.NV_FTa1.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.FTa1_Expn.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.16807.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (347868 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.FTa1_Expn.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.18449.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (347868 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear.adjusted
.
74 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.07355.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (344914 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.08343.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (347868 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear.adjusted
.
120 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.SOC1c.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.05718.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (351426 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.SOC1c.assoc.linear.adjusted
.
48 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.SOC1c_V.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.00325.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (330994 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr4-filtered-set-2014Apr15.SOC1c_V.assoc.linear.adjusted
.

            Performing QC steps on genotype file: chr5-filtered-set-2014Apr15.bcf
        PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to qc_genotypes.log.
Options in effect:
  --allow-extra-chr
  --bcf /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Genotypes/chr5-filtered-set-2014Apr15.bcf
  --const-fid
  --geno 0.1
  --keep /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined
  --maf 0.02
  --make-bed
  --out qc_genotypes

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--bcf: qc_genotypes-temporary.bed + qc_genotypes-temporary.bim +
qc_genotypes-temporary.fam written.
4496375 variants loaded from .bim file.
262 people (0 males, 0 females, 262 ambiguous) loaded from .fam.
Ambiguous sex IDs written to qc_genotypes.nosex .
--keep: 225 people remaining.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate in remaining samples is 0.755266.
3154985 variants removed due to missing genotype data (--geno).
1055910 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
285480 variants and 225 people pass filters and QC.
Note: No phenotypes present.
--make-bed to qc_genotypes.bed + qc_genotypes.bim + qc_genotypes.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%Estimating population structure...done.
PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to population_structure.log.
Options in effect:
  --bfile qc_genotypes
  --out population_structure
  --pca 10

15488 MB RAM detected; reserving 7744 MB for main workspace.
285480 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to population_structure.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.938745.
285480 variants and 225 people pass filters and QC.
Note: No phenotypes present.

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Relationship matrix calculation complete.
[extracting eigenvalues and eigenvectors]
--pca: Results saved to population_structure.eigenval and
population_structure.eigenvec .
Performing association test...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.log.
Options in effect:
  --adjust
  --all-pheno
  --allow-no-sex
  --bfile qc_genotypes
  --covar population_structure.eigenvec
  --linear
  --out /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15
  --pheno /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined

15488 MB RAM detected; reserving 7744 MB for main workspace.
285480 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.nosex
.
225 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked.
--covar: 10 covariates loaded.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.938745.
285480 variants and 225 people pass filters and QC.
Phenotype data is quantitative.
225 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.GH2_FlDate.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.30298.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (285480 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.GH2_FlDate.assoc.linear.adjusted
.
56 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.nodestofloweringV.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (269694 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.nodestofloweringV.assoc.linear.adjusted
.
86 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.NV_FTa1.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.04494.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (280295 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.NV_FTa1.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.FTa1_Expn.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.08851.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (280619 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.FTa1_Expn.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.07746.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (280619 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear.adjusted
.
74 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (277848 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.10583.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (280619 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear.adjusted
.
120 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.SOC1c.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.06632.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (283671 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.SOC1c.assoc.linear.adjusted
.
48 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.SOC1c_V.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (266550 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr5-filtered-set-2014Apr15.SOC1c_V.assoc.linear.adjusted
.

            Performing QC steps on genotype file: chr6-filtered-set-2014Apr15.bcf
        PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to qc_genotypes.log.
Options in effect:
  --allow-extra-chr
  --bcf /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Genotypes/chr6-filtered-set-2014Apr15.bcf
  --const-fid
  --geno 0.1
  --keep /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined
  --maf 0.02
  --make-bed
  --out qc_genotypes

15488 MB RAM detected; reserving 7744 MB for main workspace.

--bcf: 1k variants complete.
--bcf: 2k variants complete.
--bcf: 3k variants complete.
--bcf: 4k variants complete.
--bcf: 5k variants complete.
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--bcf: 29k variants complete.
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--bcf: 38k variants complete.
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--bcf: 49k variants complete.
--bcf: 50k variants complete.
--bcf: 51k variants complete.
--bcf: 52k variants complete.
--bcf: 53k variants complete.
--bcf: 54k variants complete.
--bcf: 55k variants complete.
--bcf: 56k variants complete.
--bcf: 57k variants complete.
--bcf: 58k variants complete.
--bcf: 59k variants complete.
--bcf: 60k variants complete.
--bcf: 61k variants complete.
--bcf: 62k variants complete.
--bcf: 63k variants complete.
--bcf: 64k variants complete.
--bcf: 65k variants complete.
--bcf: 66k variants complete.
--bcf: 67k variants complete.
--bcf: 68k variants complete.
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--bcf: 70k variants complete.
--bcf: 71k variants complete.
--bcf: 72k variants complete.
--bcf: 73k variants complete.
--bcf: 74k variants complete.
--bcf: 75k variants complete.
--bcf: 76k variants complete.
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--bcf: qc_genotypes-temporary.bed + qc_genotypes-temporary.bim +
qc_genotypes-temporary.fam written.
3650081 variants loaded from .bim file.
262 people (0 males, 0 females, 262 ambiguous) loaded from .fam.
Ambiguous sex IDs written to qc_genotypes.nosex .
--keep: 225 people remaining.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate in remaining samples is 0.71474.
2788443 variants removed due to missing genotype data (--geno).
639278 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
222360 variants and 225 people pass filters and QC.
Note: No phenotypes present.
--make-bed to qc_genotypes.bed + qc_genotypes.bim + qc_genotypes.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
Estimating population structure...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to population_structure.log.
Options in effect:
  --bfile qc_genotypes
  --out population_structure
  --pca 10

15488 MB RAM detected; reserving 7744 MB for main workspace.
222360 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to population_structure.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.937347.
222360 variants and 225 people pass filters and QC.
Note: No phenotypes present.

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Relationship matrix calculation complete.
[extracting eigenvalues and eigenvectors]Performing association test...
--pca: Results saved to population_structure.eigenval and
population_structure.eigenvec .
PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.log.
Options in effect:
  --adjust
  --all-pheno
  --allow-no-sex
  --bfile qc_genotypes
  --covar population_structure.eigenvec
  --linear
  --out /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15
  --pheno /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined

15488 MB RAM detected; reserving 7744 MB for main workspace.
222360 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.nosex
.
225 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked.
--covar: 10 covariates loaded.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.937347.
222360 variants and 225 people pass filters and QC.
Phenotype data is quantitative.
225 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.GH2_FlDate.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.15347.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (222360 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.GH2_FlDate.assoc.linear.adjusted
.
56 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.nodestofloweringV.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (209860 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.nodestofloweringV.assoc.linear.adjusted
.
86 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.NV_FTa1.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.07412.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (218256 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.NV_FTa1.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.FTa1_Expn.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.14068.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (218364 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.FTa1_Expn.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.14134.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (218364 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear.adjusted
.
74 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.02496.
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/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear.adjusted
.
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Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.10794.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (218364 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear.adjusted
.
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Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.SOC1c.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.1266.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (220820 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.SOC1c.assoc.linear.adjusted
.
48 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.SOC1c_V.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (208285 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr6-filtered-set-2014Apr15.SOC1c_V.assoc.linear.adjusted
.

            Performing QC steps on genotype file: chr7-filtered-set-2014Apr15.bcf
        PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to qc_genotypes.log.
Options in effect:
  --allow-extra-chr
  --bcf /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Genotypes/chr7-filtered-set-2014Apr15.bcf
  --const-fid
  --geno 0.1
  --keep /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined
  --maf 0.02
  --make-bed
  --out qc_genotypes

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--bcf: qc_genotypes-temporary.bed + qc_genotypes-temporary.bim +
qc_genotypes-temporary.fam written.
4761519 variants loaded from .bim file.
262 people (0 males, 0 females, 262 ambiguous) loaded from .fam.
Ambiguous sex IDs written to qc_genotypes.nosex .
--keep: 225 people remaining.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate in remaining samples is 0.759447.
3285326 variants removed due to missing genotype data (--geno).
1163322 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
312871 variants and 225 people pass filters and QC.
Note: No phenotypes present.
--make-bed to qc_genotypes.bed + qc_genotypes.bim + qc_genotypes.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
Estimating population structure...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to population_structure.log.
Options in effect:
  --bfile qc_genotypes
  --out population_structure
  --pca 10

15488 MB RAM detected; reserving 7744 MB for main workspace.
312871 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to population_structure.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939212.
312871 variants and 225 people pass filters and QC.
Note: No phenotypes present.

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Relationship matrix calculation complete.
[extracting eigenvalues and eigenvectors]
--pca: Results saved to population_structure.eigenval and
population_structure.eigenvec .
Performing association test...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.log.
Options in effect:
  --adjust
  --all-pheno
  --allow-no-sex
  --bfile qc_genotypes
  --covar population_structure.eigenvec
  --linear
  --out /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15
  --pheno /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined

15488 MB RAM detected; reserving 7744 MB for main workspace.
312871 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.nosex
.
225 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked.
--covar: 10 covariates loaded.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939212.
312871 variants and 225 people pass filters and QC.
Phenotype data is quantitative.
225 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.GH2_FlDate.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.33742.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (312871 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.GH2_FlDate.assoc.linear.adjusted
.
56 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.nodestofloweringV.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.04891.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (295898 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.nodestofloweringV.assoc.linear.adjusted
.
86 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.NV_FTa1.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.04465.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (306687 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.NV_FTa1.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.FTa1_Expn.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.20813.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (307061 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.FTa1_Expn.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.20238.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (307061 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear.adjusted
.
74 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.11974.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (304374 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.17669.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (307061 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear.adjusted
.
120 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.SOC1c.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.12928.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (310486 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.SOC1c.assoc.linear.adjusted
.
48 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.SOC1c_V.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (293249 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr7-filtered-set-2014Apr15.SOC1c_V.assoc.linear.adjusted
.

            Performing QC steps on genotype file: chr8-filtered-set-2014Apr15.bcf
        PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to qc_genotypes.log.
Options in effect:
  --allow-extra-chr
  --bcf /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Genotypes/chr8-filtered-set-2014Apr15.bcf
  --const-fid
  --geno 0.1
  --keep /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined
  --maf 0.02
  --make-bed
  --out qc_genotypes

15488 MB RAM detected; reserving 7744 MB for main workspace.

--bcf: 1k variants complete.
--bcf: 2k variants complete.
--bcf: 3k variants complete.
--bcf: 4k variants complete.
--bcf: 5k variants complete.
--bcf: 6k variants complete.
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--bcf: qc_genotypes-temporary.bed + qc_genotypes-temporary.bim +
qc_genotypes-temporary.fam written.
4377934 variants loaded from .bim file.
262 people (0 males, 0 females, 262 ambiguous) loaded from .fam.
Ambiguous sex IDs written to qc_genotypes.nosex .
--keep: 225 people remaining.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate in remaining samples is 0.758634.
3016972 variants removed due to missing genotype data (--geno).
1080916 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
280046 variants and 225 people pass filters and QC.
Note: No phenotypes present.
--make-bed to qc_genotypes.bed + qc_genotypes.bim + qc_genotypes.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
Estimating population structure...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to population_structure.log.
Options in effect:
  --bfile qc_genotypes
  --out population_structure
  --pca 10

15488 MB RAM detected; reserving 7744 MB for main workspace.
280046 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to population_structure.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939149.
280046 variants and 225 people pass filters and QC.
Note: No phenotypes present.

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Relationship matrix calculation complete.
[extracting eigenvalues and eigenvectors]
--pca: Results saved to population_structure.eigenval and
population_structure.eigenvec .
Performing association test...PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.log.
Options in effect:
  --adjust
  --all-pheno
  --allow-no-sex
  --bfile qc_genotypes
  --covar population_structure.eigenvec
  --linear
  --out /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15
  --pheno /mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/Traits/Medicago_Normalised_Traits.combined

15488 MB RAM detected; reserving 7744 MB for main workspace.
280046 variants loaded from .bim file.
225 people (0 males, 0 females, 225 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.nosex
.
225 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked.
--covar: 10 covariates loaded.
Before main variant filters, 225 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.939149.
280046 variants and 225 people pass filters and QC.
Phenotype data is quantitative.
225 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.GH2_FlDate.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.22368.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (280046 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.GH2_FlDate.assoc.linear.adjusted
.
56 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.nodestofloweringV.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.02333.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (265955 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.nodestofloweringV.assoc.linear.adjusted
.
86 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.NV_FTa1.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.04459.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (273900 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.NV_FTa1.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.FTa1_Expn.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.13052.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (275156 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.FTa1_Expn.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.12228.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (275156 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.FTa1_V_Lessexcllines.assoc.linear.adjusted
.
74 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.04149.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (272602 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.FTa2_Q_V_AA_AF.assoc.linear.adjusted
.
85 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.0207.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (275156 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.FTb1_qPCR.assoc.linear.adjusted
.
120 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.SOC1c.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.09564.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (278173 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.SOC1c.assoc.linear.adjusted
.
48 phenotype values present after --pheno.
Writing linear model association results to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.SOC1c_V.assoc.linear
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.10443.
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%--adjust values (261720 variants) written to
/mnt/DataDrive/MedicagoFiles/Analyses/Pipeline/ScratchSpace/chr8-filtered-set-2014Apr15.SOC1c_V.assoc.linear.adjusted
.

end_time <- Sys.time()
print(sprintf("Started: %s, Ended: %s", start_time, end_time))

[1] "Started: 2016-11-10 10:25:09, Ended: 2016-11-10 10:51:46"

print(sprintf("Total time take: %s", end_time - start_time))

[1] "Total time take: 26.6187488396962"

Results & Visualisations

There is no need to change anything in this cell. Please run (important if you want to save your results!). For each trait this cell will:

• merge the association results from all chromosomes into a single file. The merged file will be saved to the Results directory.
  
• produce a Q-Q plot for e

for (trait_ in all_traits) {
    
    cat(sprintf("
    #
    # Trait: %s
    #
    ", trait_))
    
    
    lcl_trait <- strsplit(trait_, "\\.")[[1]][1]
    
    # QC plots 
    # --------
    #   a) merge the unadjusted pvalues from each chromosome's results files
    #   b) save a Q-Q plot for each chromosome
    #   c) save a manhattan plot
    merged_results <- rbindlist(lapply(list.files(sprintf("%s/ScratchSpace", home_), 
                                                  pattern = sprintf("%s.assoc.linear$", lcl_trait),
                                                  full.names = TRUE),
                                       function (x) {
                                           tmp <- fread(x)
                                           return (tmp[TEST == "ADD"])
                                       }))
    # write merged results to Results directory
    write.csv(merged_results, sprintf("%s/Results/%s_assoc_results.csv", home_, lcl_trait),
              quote = F, row.names = F)
    
    # save Q-Q plot
    for (chr in unique(merged_results[, CHR])) {
        png(sprintf("%s/Results/Visualisations/%s_chromosome%s_QQPlot.png", home_, lcl_trait, chr))
        qq(merged_results[CHR == chr, P], main = sprintf("%s chromosome %s", lcl_trait, chr))
        dev.off()
    }
    
    # save manhattan
    png(sprintf("%s/Results/Visualisations/%s_manhattan_plot.png", home_, lcl_trait),
        height = 600, width = 1500)
    manhattan(merged_results[P < 0.001], main = sprintf("%s GWAS", lcl_trait))
    dev.off()
}

    #
    # Trait: GH2_FlDate
    #

    
Read 58.8% of 3518097 rows
Read 3518097 rows and 9 (of 9) columns from 0.272 GB file in 00:00:03

Read 76.5% of 3122174 rows
Read 3122174 rows and 9 (of 9) columns from 0.241 GB file in 00:00:03

Read 61.2% of 3841772 rows
Read 3841772 rows and 9 (of 9) columns from 0.297 GB file in 00:00:03

Read 63.7% of 3895375 rows
Read 3895375 rows and 9 (of 9) columns from 0.301 GB file in 00:00:03

Read 82.2% of 3140280 rows
Read 3140280 rows and 9 (of 9) columns from 0.243 GB file in 00:00:03

Read 70.3% of 3441581 rows
Read 3441581 rows and 9 (of 9) columns from 0.266 GB file in 00:00:03

Read 83.8% of 3080506 rows
Read 3080506 rows and 9 (of 9) columns from 0.238 GB file in 00:00:03

    #
    # Trait: nodestofloweringV
    #

    
Read 69.9% of 3518097 rows
Read 3518097 rows and 9 (of 9) columns from 0.272 GB file in 00:00:03

Read 90.0% of 3122174 rows
Read 3122174 rows and 9 (of 9) columns from 0.241 GB file in 00:00:03

Read 63.3% of 3841772 rows
Read 3841772 rows and 9 (of 9) columns from 0.297 GB file in 00:00:03

Read 60.3% of 3895375 rows
Read 3895375 rows and 9 (of 9) columns from 0.301 GB file in 00:00:03

Read 79.0% of 3140280 rows
Read 3140280 rows and 9 (of 9) columns from 0.243 GB file in 00:00:03

Read 75.3% of 3441581 rows
Read 3441581 rows and 9 (of 9) columns from 0.266 GB file in 00:00:03

Read 82.8% of 3080506 rows
Read 3080506 rows and 9 (of 9) columns from 0.238 GB file in 00:00:03

    #
    # Trait: NV_FTa1
    #

    
Read 72.8% of 3518097 rows
Read 3518097 rows and 9 (of 9) columns from 0.272 GB file in 00:00:03

Read 84.9% of 3122174 rows
Read 3122174 rows and 9 (of 9) columns from 0.241 GB file in 00:00:03

Read 64.6% of 3841772 rows
Read 3841772 rows and 9 (of 9) columns from 0.297 GB file in 00:00:03

Read 59.3% of 3895375 rows
Read 3895375 rows and 9 (of 9) columns from 0.301 GB file in 00:00:03

Read 82.8% of 3140280 rows
Read 3140280 rows and 9 (of 9) columns from 0.243 GB file in 00:00:03

Read 74.4% of 3441581 rows
Read 3441581 rows and 9 (of 9) columns from 0.266 GB file in 00:00:03

Read 84.1% of 3080506 rows
Read 3080506 rows and 9 (of 9) columns from 0.238 GB file in 00:00:03

    #
    # Trait: FTa1_Expn
    #

    
Read 79.9% of 3518097 rows
Read 3518097 rows and 9 (of 9) columns from 0.272 GB file in 00:00:03

Read 91.6% of 3122174 rows
Read 3122174 rows and 9 (of 9) columns from 0.241 GB file in 00:00:03

Read 68.7% of 3841772 rows
Read 3841772 rows and 9 (of 9) columns from 0.297 GB file in 00:00:03

Read 62.4% of 3895375 rows
Read 3895375 rows and 9 (of 9) columns from 0.301 GB file in 00:00:03

Read 89.2% of 3140280 rows
Read 3140280 rows and 9 (of 9) columns from 0.243 GB file in 00:00:03

Read 80.5% of 3441581 rows
Read 3441581 rows and 9 (of 9) columns from 0.266 GB file in 00:00:03

Read 88.0% of 3080506 rows
Read 3080506 rows and 9 (of 9) columns from 0.238 GB file in 00:00:03

    #
    # Trait: FTa1_V_Lessexcllines
    #

    
Read 75.6% of 3518097 rows
Read 3518097 rows and 9 (of 9) columns from 0.272 GB file in 00:00:03

Read 87.4% of 3122174 rows
Read 3122174 rows and 9 (of 9) columns from 0.241 GB file in 00:00:03

Read 64.6% of 3841772 rows
Read 3841772 rows and 9 (of 9) columns from 0.297 GB file in 00:00:03

Read 60.6% of 3895375 rows
Read 3895375 rows and 9 (of 9) columns from 0.301 GB file in 00:00:03

Read 84.4% of 3140280 rows
Read 3140280 rows and 9 (of 9) columns from 0.243 GB file in 00:00:03

Read 70.6% of 3441581 rows
Read 3441581 rows and 9 (of 9) columns from 0.266 GB file in 00:00:03

Read 86.3% of 3080506 rows
Read 3080506 rows and 9 (of 9) columns from 0.238 GB file in 00:00:03

    #
    # Trait: FTa2_Q_V_AA_AF
    #

    
Read 74.2% of 3518097 rows
Read 3518097 rows and 9 (of 9) columns from 0.272 GB file in 00:00:03

Read 75.9% of 3122174 rows
Read 3122174 rows and 9 (of 9) columns from 0.241 GB file in 00:00:03

Read 63.3% of 3841772 rows
Read 3841772 rows and 9 (of 9) columns from 0.297 GB file in 00:00:03

Read 61.9% of 3895375 rows
Read 3895375 rows and 9 (of 9) columns from 0.301 GB file in 00:00:03

Read 85.0% of 3140280 rows
Read 3140280 rows and 9 (of 9) columns from 0.243 GB file in 00:00:03

Read 71.8% of 3441581 rows
Read 3441581 rows and 9 (of 9) columns from 0.266 GB file in 00:00:03

Read 86.3% of 3080506 rows
Read 3080506 rows and 9 (of 9) columns from 0.238 GB file in 00:00:03

    #
    # Trait: FTb1_qPCR
    #

    
Read 76.2% of 3518097 rows
Read 3518097 rows and 9 (of 9) columns from 0.272 GB file in 00:00:03

Read 84.6% of 3122174 rows
Read 3122174 rows and 9 (of 9) columns from 0.241 GB file in 00:00:03

Read 58.0% of 3841772 rows
Read 100.0% of 3841772 rows
Read 3841772 rows and 9 (of 9) columns from 0.297 GB file in 00:00:04

Read 58.0% of 3895375 rows
Read 3895375 rows and 9 (of 9) columns from 0.301 GB file in 00:00:03

Read 80.2% of 3140280 rows
Read 3140280 rows and 9 (of 9) columns from 0.243 GB file in 00:00:03

Read 75.5% of 3441581 rows
Read 3441581 rows and 9 (of 9) columns from 0.266 GB file in 00:00:03

Read 86.3% of 3080506 rows
Read 3080506 rows and 9 (of 9) columns from 0.238 GB file in 00:00:03

    #
    # Trait: SOC1c
    #

    
Read 66.8% of 3518097 rows
Read 3518097 rows and 9 (of 9) columns from 0.272 GB file in 00:00:03

Read 85.8% of 3122174 rows
Read 3122174 rows and 9 (of 9) columns from 0.241 GB file in 00:00:03

Read 65.6% of 3841772 rows
Read 3841772 rows and 9 (of 9) columns from 0.297 GB file in 00:00:03

Read 62.1% of 3895375 rows
Read 3895375 rows and 9 (of 9) columns from 0.301 GB file in 00:00:03

Read 87.9% of 3140280 rows
Read 3140280 rows and 9 (of 9) columns from 0.243 GB file in 00:00:03

Read 78.5% of 3441581 rows
Read 3441581 rows and 9 (of 9) columns from 0.266 GB file in 00:00:03

Read 87.0% of 3080506 rows
Read 3080506 rows and 9 (of 9) columns from 0.238 GB file in 00:00:03

    #
    # Trait: SOC1c_V
    #

    
Read 77.9% of 3518097 rows
Read 3518097 rows and 9 (of 9) columns from 0.272 GB file in 00:00:03

Read 86.2% of 3122174 rows
Read 3122174 rows and 9 (of 9) columns from 0.241 GB file in 00:00:03

Read 60.4% of 3841772 rows
Read 3841772 rows and 9 (of 9) columns from 0.297 GB file in 00:00:03

Read 63.4% of 3895375 rows
Read 3895375 rows and 9 (of 9) columns from 0.301 GB file in 00:00:03

Read 91.7% of 3140280 rows
Read 3140280 rows and 9 (of 9) columns from 0.243 GB file in 00:00:03

Read 77.0% of 3441581 rows
Read 3441581 rows and 9 (of 9) columns from 0.266 GB file in 00:00:03

Read 93.5% of 3080506 rows
Read 3080506 rows and 9 (of 9) columns from 0.238 GB file in 00:00:03